Make sure you Bios is Set to CDROM first boot ,put the windows cd in the drive ,boot computer,go lie as if you were going to install windows again ,and format the partition with the latest install .maybe!

Was the new instance of Windows XP installed on a different drive or partition? If so, you can delete the WINDOWS folder on that drive or partition, and then disable the multi-boot request by right-clicking 'My computer', choosing Properties->Advanced->Startup->Settings, selecting the correct entry from the list of operating systems to boot from, and then disabling the 'Time to display' setting.

Your system will then boot from the original installation, without displaying a multi-boot menu.

But I would strongly suggest you wipe your system clean and install fresh, to correct any installation corruption you might have. (After all, why were you trying to refresh install in the fist place?) You'll find helpful guides linked in my sig.

But, if you wish to do a refresh install after you've removed the second, unwanted Windows installation, follow Microsoft's guide for performing an In Place upgrade.